Abstract

We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of 140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

References

  1. 1.

    , & Acc. Chem. Res. 45, 196–205 (2012).

  2. 2.

    , & J. Am. Chem. Soc. 129, 14739–14745 (2007).

  3. 3.

    & Nucleic Acids Res. 32, 4269–4280 (2004).

  4. 4.

    et al. Biophys. J. 92, 3817–3829 (2007).

  5. 5.

    et al. J. Chem. Theory Comput. 9, 2339–2354 (2013).

  6. 6.

    et al. J. Chem. Theory Comput. 8, 2506–2520 (2012).

  7. 7.

    et al. Nature 287, 755–758 (1980).

  8. 8.

    et al. Nucleic Acids Res. 38, 299–313 (2010).

  9. 9.

    , , , & Nucleic Acids Res. 40, 10668–10678 (2012).

  10. 10.

    , , , & Nucleic Acids Res. 38, 3414–3422 (2010).

  11. 11.

    , , & Nucleic Acids Res. 9, 5443–5458 (1981).

  12. 12.

    , , & Biochemistry 43, 4092–4100 (2004).

  13. 13.

    , & J. Am. Chem. Soc. 123, 12018–12025 (2001).

  14. 14.

    & Triple-helical Nucleic Acids 1st edn. (Springer-Verlag, 1996).

  15. 15.

    et al. J. Chem. Theory Comput. 5, 2514–2530 (2009).

  16. 16.

    et al. J. Am. Chem. Soc. 135, 5344–5347 (2013).

  17. 17.

    , , , & Proc. Natl. Acad. Sci. USA 95, 11163–11168 (1998).

  18. 18.

    , , & Nucleic Acids Res. 36, 2379–2394 (2008).

  19. 19.

    & Proc. Natl. Acad. Sci. USA 94, 14418–14422 (1997).

  20. 20.

    , & Nucleic Acids Res. 36, 1120–1128 (2008).

  21. 21.

    , & J. Am. Chem. Soc. 126, 10142–10151 (2004).

  22. 22.

    , , , & J. Comput. Chem. 18, 1136–1150 (1997).

  23. 23.

    et al. Chemistry 12, 2854–2865 (2006).

  24. 24.

    & Chem. Phys. 182, 237–248 (1994).

  25. 25.

    , & J. Am. Chem. Soc. 118, 6811–6821 (1996).

  26. 26.

    , , , & in Computational Chemistry: Reviews of Current Trends Vol. 4 (ed. Leszczynski, J.) 191–225 (World Scientific Publishing, 1999).

  27. 27.

    et al. Chemistry 11, 5062–5066 (2005).

  28. 28.

    et al. Biophys. J. 87, 3799–3813 (2004).

  29. 29.

    , , & J. Am. Chem. Soc. 136, 3075–3086 (2014).

  30. 30.

    , , & J. Chem. Phys. 72, 650–654 (1980).

  31. 31.

    & J. Chem. Phys. 98, 1358–1371 (1993).

  32. 32.

    et al. Chem. Phys. Lett. 286, 243–252 (1998).

  33. 33.

    , , , & Chem. Phys. Lett. 302, 437–446 (1999).

  34. 34.

    , & Chem. Phys. 55, 117–129 (1981).

  35. 35.

    & Chem. Phys. 65, 239–245 (1982).

  36. 36.

    , & J. Chem. Phys. 107, 3032–3041 (1997).

  37. 37.

    , & J. Comput. Chem. 15, 446–454 (1994).

  38. 38.

    , , , & J. Mol. Struct. THEOCHEM 727, 29–40 (2005).

  39. 39.

    , , & J. Phys. Chem. B 113, 9330–9334 (2009).

  40. 40.

    , & J. Comput. Aided Mol. Des. 24, 281–291 (2010).

  41. 41.

    , & J. Phys. Chem. B 113, 6378–6396 (2009).

  42. 42.

    & J. Comput. Phys. 23, 187–199 (1977).

  43. 43.

    et al. J. Chem. Theory Comput. 8, 348–362 (2012).

  44. 44.

    , , , & J. Biomol. NMR 26, 297–315 (2003).

  45. 45.

    et al. J. Chem. Theory Comput. 7, 2886–2902 (2011).

  46. 46.

    , , & J. Chem. Theory Comput. 4, 435–447 (2008).

  47. 47.

    , & Nat. Commun. 5, 5152 (2014).

  48. 48.

    , & J. Comput. Phys. 23, 327–341 (1977).

  49. 49.

    , , & J. Comput. Chem. 18, 1463–1472 (1997).

  50. 50.

    , , , & J. Chem. Phys. 79, 926–935 (1983).

  51. 51.

    , & J. Phys. Chem. 91, 6269–6271 (1987).

  52. 52.

    & J. Chem. Phys. 100, 3757–3766 (1994).

  53. 53.

    , & J. Chem. Phys. 98, 10089–10092 (1993).

  54. 54.

    , & Biochim. Biophys. Acta 1850, 1059–1071 (2015).

  55. 55.

    & Biochem. Biophys. Res. Commun. 47, 1504–1509 (1972).

  56. 56.

    , , & Chem. Soc. Rev. 32, 350–364 (2003).

  57. 57.

    et al. J. Chem. Theory Comput. 1, 790–800 (2005).

  58. 58.

    , & Proteins 17, 412–425 (1993).

  59. 59.

    , , & J. Mol. Biol. 299, 695–709 (2000).

  60. 60.

    , , , & J. Mol. Biol. 343, 627–638 (2004).

  61. 61.

    & J. Chem. Phys. 115, 6289–6292 (2001).

  62. 62.

    Chem. Phys. Lett. 215, 617–621 (1993).

  63. 63.

    Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics 62, 8438 (2000).

  64. 64.

    & Phys. Rev. Lett. 109, 228101 (2012).

  65. 65.

    , , & Phys. Chem. Chem. Phys. 12, 1399–1406 (2010).

  66. 66.

    et al. Proc. Natl. Acad. Sci. USA 111, E3624–E3630 (2014).

  67. 67.

    , , & Biophys. J. 69, 1519–1527 (1995).

  68. 68.

    et al. Bioinformatics 28, 1278–1279 (2012).

  69. 69.

    et al. Nucleic Acids Res. 41, W47–W55 (2013).

  70. 70.

    , , , & Nucleic Acids Res. 37, 5917–5929 (2009).

  71. 71.

    Nat. Protoc. 3, 679–690 (2008).

  72. 72.

    et al. Eur. J. Biochem. 80, 319–324 (1977).

  73. 73.

    & J. Magn. Reson. 87, 475–487 (1990).

  74. 74.

    , & J. Chem. Phys. 125, 084902 (2006).

  75. 75.

    & BMC Res. Notes 5, 367 (2012).

Download references

Acknowledgements

M.O. thanks the Spanish Ministry of Science (BIO2012-32868), the Catalan SGR, the Instituto Nacional de Bioinformática and the European Research Council (ERC SimDNA) for support. M.O. is an academia researcher in the Catalan Institution for Research and Advanced Studies (ICREA). M.O. thanks the Barcelona Supercomputing Center for CPU and GPU time on MareNostrum and MinoTauro. C.A.L., S.A.H. and A.N. thank the UK HECBioSim Consortium for time on the ARCHER high-performance computing system (grant EP-L000253-1). A.N. was supported by the Biotechnology and Biological Sciences Research Council (BBSRC; grant BB-I019294-1) and thanks ARC Leeds for computational resources. P.D.D. is a PEDECIBA (Programa de Desarrollo de las Ciencias Básicas) and SNI (Sistema Nacional de Investigadores; ANII, Uruguay) researcher. D.A.C. thanks C. Liu for assistance with the crystal simulation analysis.

Author information

Affiliations

  1. Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain.

    • Ivan Ivani
    • , Pablo D Dans
    • , Ignacio Faustino
    • , Adam Hospital
    • , Jürgen Walther
    • , Alexandra Balaceanu
    • , Guillem Portella
    • , Federica Battistini
    •  & Modesto Orozco
  2. Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.

    • Ivan Ivani
    • , Pablo D Dans
    • , Ignacio Faustino
    • , Adam Hospital
    • , Jürgen Walther
    • , Pau Andrio
    • , Ramon Goñi
    • , Alexandra Balaceanu
    • , Guillem Portella
    • , Federica Battistini
    • , Josep Lluis Gelpí
    •  & Modesto Orozco
  3. School of Physics and Astronomy, University of Leeds, Leeds, UK.

    • Agnes Noy
    •  & Sarah A Harris
  4. Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.

    • Alberto Pérez
  5. Barcelona Supercomputing Center, Barcelona, Spain.

    • Pau Andrio
    •  & Ramon Goñi
  6. Department of Chemistry, University of Cambridge, Cambridge, UK.

    • Guillem Portella
    •  & Michele Vendruscolo
  7. Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain.

    • Josep Lluis Gelpí
    •  & Modesto Orozco
  8. Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Cientificas, Madrid, Spain.

    • Carlos González
  9. School of Pharmacy, University of Nottingham, Nottingham, UK.

    • Charles A Laughton
  10. Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK.

    • Charles A Laughton
  11. Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.

    • David A Case

Authors

  1. Search for Ivan Ivani in:

  2. Search for Pablo D Dans in:

  3. Search for Agnes Noy in:

  4. Search for Alberto Pérez in:

  5. Search for Ignacio Faustino in:

  6. Search for Adam Hospital in:

  7. Search for Jürgen Walther in:

  8. Search for Pau Andrio in:

  9. Search for Ramon Goñi in:

  10. Search for Alexandra Balaceanu in:

  11. Search for Guillem Portella in:

  12. Search for Federica Battistini in:

  13. Search for Josep Lluis Gelpí in:

  14. Search for Carlos González in:

  15. Search for Michele Vendruscolo in:

  16. Search for Charles A Laughton in:

  17. Search for Sarah A Harris in:

  18. Search for David A Case in:

  19. Search for Modesto Orozco in:

Contributions

I.I. derived the parmbsc1 force-field parameter set. I.I., P.D.D., A.N., A.P., I.F., A.H., J.W., A.B., G.P., F.B., C.A.L. and S.A.H. performed validation simulations. C.G., M.V. and G.P. validated results from NMR-based experiments. C.G. obtained de novo NMR spectroscopy measurements. D.A.C. performed crystal MD simulations. R.G., P.A., A.H. and J.L.G. created the database infrastructure and web application. All authors contributed to data analysis. M.O. had the idea for the study, directed the project and wrote the manuscript, which was improved by the rest of the authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Modesto Orozco.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–31, Supplementary Tables 1–12 and Supplementary Discussion

Zip files

  1. 1.

    Supplementary Software

    Parmbsc1 parameters

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nmeth.3658

Further reading